GNU bug report logs - #65493
[PATCH] gnu: Add r-msigdb.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add r-msigdb.
Date: Thu, 24 Aug 2023 10:38:37 +0000

* gnu/packages/bioconductor.scm (r-msigdb): New variable.
---
 gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 74071900a3..5e323d11ef 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1754,6 +1754,39 @@ (define-public r-msdata
 files for various search engines.")
     (license license:gpl2+)))
 
+(define-public r-msigdb
+  (package
+    (name "r-msigdb")
+    (version "1.8.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "msigdb" version
+                                     'experiment))
+              (sha256
+               (base32
+                "1kgsqg1d5r852qas09g6fs0pcmk6jgbb6g983v6iqw19qsiy6jby"))))
+    (properties `((upstream-name . "msigdb")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationdbi
+                             r-annotationhub
+                             r-experimenthub
+                             r-gseabase
+                             r-org-hs-eg-db
+                             r-org-mm-eg-db))
+    (native-inputs (list r-knitr))
+    (home-page "https://davislaboratory.github.io/msigdb")
+    (synopsis "ExperimentHub package for the molecular signatures database")
+    (description
+     "R-msigdb provides the Molecular Signatures Database in a R accessible objects.
+Signatures are stored in @code{GeneSet} class objects form
+the GSEABase package and the entire database is stored in a
+@code{GeneSetCollection} object.  These data are then hosted
+on the @code{ExperimentHub.} Data used in this package was
+obtained from the @code{MSigDB} of the Broad Institute.
+Metadata for each gene set is stored along with the gene
+set in the @code{GeneSet} class object.")
+    (license license:cc-by4.0)))
+
 (define-public r-pasilla
   (package
     (name "r-pasilla")

base-commit: 160f78a4d92205df986ed9efcce7d3aac188cb24
-- 
2.34.1

Message #10 received at 65493-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 65493-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-msigdb.
Date: Mon, 28 Aug 2023 10:06:47 +0200

Applied with minor changes:

- changed the home page because it is not reachable (guix lint
  complained)
- reflowed the description

Thanks!

-- 
Ricardo

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